Question: Issue converting VCF to MAF using snpEff annotations
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Marina Manrique • 1.3k wrote:
Hi there!
I'm trying to convert my VCF to MAF using snpEff for the annotations but I'm getting these errors (I'm copying just a set of them but I'm getting the same errors for every variant called in the VCF)
Use of uninitialized value $effect in pattern match (m//) at vcf2maf.pl line 772, <GEN1> line 2259. Use of uninitialized value $effect in string eq at vcf2maf.pl line 773, <GEN1> line 2259. Use of uninitialized value $effect in string eq at vcf2maf.pl line 774, <GEN1> line 2259. Use of uninitialized value $effect in string eq at vcf2maf.pl line 775, <GEN1> line 2259. Use of uninitialized value $effect in string eq at vcf2maf.pl line 776, <GEN1> line 2259. Use of uninitialized value $effect in pattern match (m//) at vcf2maf.pl line 777, <GEN1> line 2259. Use of uninitialized value $effect in string eq at vcf2maf.pl line 778, <GEN1> line 2259. Use of uninitialized value $effect in string eq at vcf2maf.pl line 779, <GEN1> line 2259. Use of uninitialized value $effect in pattern match (m//) at vcf2maf.pl line 780, <GEN1> line 2259. Use of uninitialized value $effect in pattern match (m//) at vcf2maf.pl line 781, <GEN1> line 2259. Use of uninitialized value $effect in pattern match (m//) at vcf2maf.pl line 782, <GEN1> line 2259. Use of uninitialized value $effect in pattern match (m//) at vcf2maf.pl line 783, <GEN1> line 2259. Use of uninitialized value $effect in pattern match (m//) at vcf2maf.pl line 784, <GEN1> line 2259. Use of uninitialized value $effect in string eq at vcf2maf.pl line 785, <GEN1> line 2259. Use of uninitialized value $effect in pattern match (m//) at vcf2maf.pl line 786, <GEN1> line 2259. Use of uninitialized value $effect in string eq at vcf2maf.pl line 787, <GEN1> line 2259. Use of uninitialized value $effect in string eq at vcf2maf.pl line 788, <GEN1> line 2259.
I'm using this script vcf2maf https://github.com/ckandoth/vcf2maf and this command
perl vcf2maf.pl --input-vcf MMB34.vcf --output-maf MMB34.maf --snpeff-path /home/ec2-user/snpEff --snpeff-data /home/ec2-user/snpEff/data --use-snpeff --ref-fasta /media/ephemeral0/.vep/homo_sapiens/76_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa
Any ideas of what I'm doing wrong?
Thanks!
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modified 9 months ago
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tsy19900929 • 0
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6.0 years ago by
Marina Manrique • 1.3k
Hi,
Kindly share how to got around this. I have vcf files that were annotated using snpeff and I would like to convert them to maf using vcf2maf.
I used:
"perl vcf2maf.pl --input-vcf file.vcf --output-maf file.maf --ref-fasta ~/GRCh37-lite.fa --species homo_sapiens --tumor-id ddd --normal-id dddnn"
I get the following errors:
Use of uninitialized value in list assignment at ~/vcf2maf.pl line 649, <gen4> line 2186.
Use of uninitialized value in list assignment at ~/vcf2maf.pl line 649, <gen4> line 2186.
Use of uninitialized value in list assignment at ~/vcf2maf.pl line 649, <gen4> line 2186.
Use of uninitialized value in list assignment at ~/vcf2maf.pl line 649, <gen4> line 2186.
Use of uninitialized value in list assignment at ~/vcf2maf.pl line 649, <gen4> line 2186.
My initial run included VEP (below) but I got wrong results when I run MutsigCV using the maf file I had generated:
"perl vcf2maf.pl --input-vcf file.vcf --output-maf file.maf --ref-fasta ~/GRCh37-lite.fa --vep-forks 4 --vep-path ~/vep --ref-fasta $VEP_DATA/homo_sapiens/86_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz --species homo_sapiens --tumor-id ddd --normal-id dddnn"
Where am I going wrong?
Thanks